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| - | [[Image:1zfx.gif|left|200px]]<br /><applet load="1zfx" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1zfx, resolution 2.38Å" /> | |
| - | '''The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site'''<br /> | |
| | | | |
| - | ==Overview== | + | ==The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site== |
| - | The hairpin ribozyme requires functional group contributions from G8 to, assist in phosphodiester bond cleavage. Previously, replacement of G8 by a, series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that, contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography, in a resolution range between 2.3 and 2.7 A. For comparison, a native, all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution., The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations, G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and, G8(uridine) folded properly, but exhibited nonideal scissile bond, geometries (tau ranging from 118 degrees to 93 degrees) that paralleled, their diminished solution activities. A superposition ensemble of all, structures, including a previously described hairpin ribozyme-vanadate, complex, indicated the scissile bond can adopt a variety of conformations, resulting from perturbation of the chemical environment and provided a, rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1, sugar pucker. In this regard, variants A8 and U8 appeared to represent, nonproductive ground states in which their 2'-OH groups mimicked the, pro-R, nonbridging oxygen of the vanadate transition-state complex., Finally, the results indicated that ordered water molecules bind near the, 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may, play an important role in the reaction. | + | <StructureSection load='1zfx' size='340' side='right'caption='[[1zfx]], [[Resolution|resolution]] 2.38Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1zfx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZFX FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfx OCA], [https://pdbe.org/1zfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zfx RCSB], [https://www.ebi.ac.uk/pdbsum/1zfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfx ProSAT]</span></td></tr> |
| | + | </table> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction. |
| | | | |
| - | ==About this Structure==
| + | Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.,Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744<ref>PMID:16411744</ref> |
| - | 1ZFX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with SO4 and NCO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZFX OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer., Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE, Biochemistry. 2006 Jan 24;45(3):686-700. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16411744 16411744]
| + | </div> |
| - | [[Category: Protein complex]]
| + | <div class="pdbe-citations 1zfx" style="background-color:#fffaf0;"></div> |
| - | [[Category: Wedekind, J.E.]]
| + | == References == |
| - | [[Category: NCO]]
| + | <references/> |
| - | [[Category: SO4]]
| + | __TOC__ |
| - | [[Category: all-rna]]
| + | </StructureSection> |
| - | [[Category: catalytic rna]]
| + | [[Category: Large Structures]] |
| - | [[Category: cobalt hexaamine]]
| + | [[Category: Wedekind JE]] |
| - | [[Category: e-loop]]
| + | |
| - | [[Category: hairpin ribozyme]]
| + | |
| - | [[Category: low salt]]
| + | |
| - | [[Category: mutation]] | + | |
| - | [[Category: ribose zipper]] | + | |
| - | [[Category: s-turn]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:52:20 2007''
| + | |
| Structural highlights
Publication Abstract from PubMed
The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction.
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.,Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE. Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744 doi:10.1021/bi051887k
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